Get run manifests from lims instead

taca/analysis/analysis_element.py

@@ -28,23 +28,25 @@ def _process(run):
             if run.status_changed(current_run_status):
                 run.update_statusdb(current_run_status) #TODO: what info needs to be gathered and uploaded?
         elif sequencing_done and demultiplexing_status == "not started": # Sequencing done. Start demux
-            if not run.manifest_exists():
+            if not run.manifest_exists(): #TODO: this should check for the zip file in lims output location
                 logger.warn(f"Run manifest is missing for {run.flowcell_id}")
                 #TODO: email operator warning
                 return
             elif run.manifest_exists():
-                sample_info = run.get_sample_info_from_manifest()
-                sample_types = run.get_sample_types(sample_info)
-                if len(sample_types) == 1:
-                    run.start_demux()
-                elif len(sample_types) > 1:
-                    for sample_type in sample_types:
-                        run.make_manifest(sample_info, sample_type)
-                        run.start_demux()
-                else:
-                    logger.warn(f"No samples were found in the sample manifest for run {run.flowcell_id}.")
-                    #TODO: email operator warning
-                    return
+                os.mkdir(run.demux_dir)
+                run.copy_manifests()
+                run_manifests = glob.glob(
+                    os.path.join(run.run_dir, "RunManifest_*.csv")
+                    )  # TODO: is this filename right?
+                sub_demux_count = 0
+                for run_manifest in run_manifests.sort():
+                    if len(run_manifests) == 1:
+                        demux_dir = run.demux_dir
+                    elif len(run_manifests) > 1:
+                        demux_dir = f"Demultiplexing_{sub_demux_count}"
+                    os.mkdir(demux_dir)
+                    run.start_demux(run_manifest, demux_dir)
+                    sub_demux_count += 1
                 current_run_status = "demultiplexing"
                 if run.status_changed(current_run_status):
                     run.update_statusdb(current_run_status)
@@ -56,6 +58,8 @@ def _process(run):
         elif sequencing_done and demultiplexing_status == "finished":
             transfer_file = CONFIG.get('Element').get('Aviti').get('transfer_log')
             if not run.is_transferred(transfer_file) and not run.transfer_ongoing():
+                #TODO: if multiple demux dirs, aggregate the results into Demultiplexing?
+                run.aggregate_demux_results
                 run.sync_metadata()
                 run.make_transfer_indicator()
                 current_run_status = "transferring"

taca/element/Element_Runs.py

@@ -57,19 +57,11 @@ def update_statusdb(self, current_run_status):
         pass
 
     def manifest_exists(self):
-        return os.path.isfile(self.run_manifest_file)
+        return os.path.isfile(self.run_manifest_file) #TODO: still true?
 
-    def get_sample_info_from_manifest(self):
-        sample_info = {} #TODO: populate with sample info from manifest
-        return sample_info
-
-    def get_sample_types(self, sample_info):
-        sample_types = () #TODO: populate 
-        return sample_types
-
-    def make_manifest(self, sample_info, sample_type):
-        #TODO: make a manifest for a sample_type based on sample_info
-        return
+    def copy_manifests():
+        #TODO: copy manifest zip file from lims location and unzip
+        pass
 
     def generate_demux_command(self):
         command = [
@@ -82,7 +74,7 @@ def generate_demux_command(self):
         ]
         return command
 
-    def start_demux(self):
+    def start_demux(self, run_manifest, demux_dir):
         with chdir(self.run_dir):
             cmd = self.generate_demux_command()
             misc.call_external_command_detached(